Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020183.1 Corchorus olitorius cultivar O-4 contig20216, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27284
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:5296 original size:58 final size:58
Alignment explanation
Indices: 5170--5402 Score: 324
Period size: 58 Copynumber: 4.0 Consensus size: 58
5160 TTGGTTGTAT
* * *
5170 GACCTAGTGGGCATCCCCCA-TACGTGCAATGAGAATGATCGAGCATCCCTCGGTCGCAC
1 GACCCAGTGGGCATCCCCCACT-CGTGCAATAAGAA-AATCGAGCATCCCTCGGTCGCAC
* *
5229 GACCTAGTGGGCATCCCCCACTCGTGCAATAAGAAAATCGAGCATCCCTCGGTCGTAC
1 GACCCAGTGGGCATCCCCCACTCGTGCAATAAGAAAATCGAGCATCCCTCGGTCGCAC
* * * * *
5287 GACCCAGTGGGCATGCCCCACTCATGCAATAAGAAAATCGAGTATCCCTCGTTCACAC
1 GACCCAGTGGGCATCCCCCACTCGTGCAATAAGAAAATCGAGCATCCCTCGGTCGCAC
* * *
5345 GACCCAATGGGCATCCCCCACTCGTGCAAAAAGAAAAACGAGCATCCCTCGGTCGCAC
1 GACCCAGTGGGCATCCCCCACTCGTGCAATAAGAAAATCGAGCATCCCTCGGTCGCAC
5403 AACCTAAAAT
Statistics
Matches: 155, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
58 122 0.79
59 32 0.21
60 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.17
Consensus pattern (58 bp):
GACCCAGTGGGCATCCCCCACTCGTGCAATAAGAAAATCGAGCATCCCTCGGTCGCAC
Found at i:10121 original size:27 final size:27
Alignment explanation
Indices: 10063--10137 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 27
10053 CTCGTATTTG
*
10063 GGCCCGAAAAAGCATTTA-TT-TTTTT
1 GGCCCAAAAAAGCATTTATTTATTTTT
10088 GGCCCAAAAAAGCATTTATTTATTTTT
1 GGCCCAAAAAAGCATTTATTTATTTTT
10115 GGCCCAAAAAAGCATTTGATTTA
1 GGCCCAAAAAAGCATTT-ATTTA
10138 GGAATATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 17 0.37
26 2 0.04
27 22 0.48
28 5 0.11
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (27 bp):
GGCCCAAAAAAGCATTTATTTATTTTT
Found at i:11781 original size:22 final size:24
Alignment explanation
Indices: 11755--11802 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
11745 GTTTTCTGCA
*
11755 TTAAGAAATCGTTT-TACTG-TTT
1 TTAAGAAAGCGTTTCTACTGATTT
*
11777 TTAAGAAAGCTTTTCTACTGATTT
1 TTAAGAAAGCGTTTCTACTGATTT
11801 TT
1 TT
11803 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 5 0.23
24 5 0.23
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.50
Consensus pattern (24 bp):
TTAAGAAAGCGTTTCTACTGATTT
Found at i:12803 original size:25 final size:25
Alignment explanation
Indices: 12771--12818 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
12761 CTTTTTATGA
*
12771 GGGAATTTAAAAGTAACTAATATAG
1 GGGAATTTAAAAGTAAATAATATAG
12796 GGGAATTTAAAAGTAAATAATAT
1 GGGAATTTAAAAGTAAATAATAT
12819 GAACAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.19, T:0.29
Consensus pattern (25 bp):
GGGAATTTAAAAGTAAATAATATAG
Found at i:14278 original size:24 final size:23
Alignment explanation
Indices: 14250--14295 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
14240 GTTATTAGAC
14250 AAGAAAGAA-TAGATCAAAAGTTAG
1 AAGAAA-AATTAGAT-AAAAGTTAG
14274 AAGAAAAATTTAGATAAAAGTT
1 AAGAAAAA-TTAGATAAAAGTT
14296 GATGGCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 2 0.10
24 13 0.65
25 5 0.25
ACGTcount: A:0.59, C:0.02, G:0.17, T:0.22
Consensus pattern (23 bp):
AAGAAAAATTAGATAAAAGTTAG
Found at i:20757 original size:17 final size:17
Alignment explanation
Indices: 20735--20769 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20725 GTTGTTAAAA
20735 CTATGAATTTCTTTCCT
1 CTATGAATTTCTTTCCT
20752 CTATGAATTTCTTTCCT
1 CTATGAATTTCTTTCCT
20769 C
1 C
20770 AATAGGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.06, T:0.51
Consensus pattern (17 bp):
CTATGAATTTCTTTCCT
Found at i:26377 original size:45 final size:42
Alignment explanation
Indices: 26313--26414 Score: 150
Period size: 45 Copynumber: 2.3 Consensus size: 42
26303 AGCAACAATT
*
26313 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGAAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT---GGAGTAG
26358 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
*
26400 AATTATTTGCTTTAT
1 AA-TATTAGCTTTAT
26415 ATACGCGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
42 9 0.17
43 11 0.20
45 34 0.63
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Done.